Gene architecture directs splicing outcome in separate nuclear spatial regions

Luna Tammer, Ofir Hameiri, Ifat Keydar, Vanessa Rachel Roy, Asaf Ashkenazy-Titelman, Noélia Custódio, Itay Sason, Ronna Shayevitch, Victoria Rodríguez-Vaello, José Rino, Galit Lev Maor, Yodfat Leader, Doha Khair, Erez Lieberman Aiden, Ran Elkon, Manuel Irimia, Roded Sharan, Yaron Shav-Tal, Maria Carmo-Fonseca, Gil Ast

Research output: Contribution to journalArticlepeer-review

25 Scopus citations

Abstract

How the splicing machinery defines exons or introns as the spliced unit has remained a puzzle for 30 years. Here, we demonstrate that peripheral and central regions of the nucleus harbor genes with two distinct exon-intron GC content architectures that differ in the splicing outcome. Genes with low GC content exons, flanked by long introns with lower GC content, are localized in the periphery, and the exons are defined as the spliced unit. Alternative splicing of these genes results in exon skipping. In contrast, the nuclear center contains genes with a high GC content in the exons and short flanking introns. Most splicing of these genes occurs via intron definition, and aberrant splicing leads to intron retention. We demonstrate that the nuclear periphery and center generate different environments for the regulation of alternative splicing and that two sets of splicing factors form discrete regulatory subnetworks for the two gene architectures. Our study connects 3D genome organization and splicing, thus demonstrating that exon and intron definition modes of splicing occur in different nuclear regions.

Original languageEnglish
Pages (from-to)1021-1034.e8
JournalMolecular Cell
Volume82
Issue number5
DOIs
StatePublished - 3 Mar 2022

Bibliographical note

Publisher Copyright:
© 2022 Elsevier Inc.

Funding

The research was funded by the Israel Science Foundation [ ISF 671/18 , ISF 142/13 , and ISF 2417/20 ]; German-Israeli Foundation for Scientific Research and Development [ GIF I-1460 ]; Israel Cancer Association [ ICA 20170034 ]; Israel Cancer Research Fund [ ICRF PG-18-105 ]; and United States – Israel Binational Science Foundation [ BSF 2017086 ]. L.T. was supported by a fellowship from the Planning & Budgeting Committee of the Council of Higher Education of Israel. O.H. and V.R.R. were supported by a fellowship from the Edmond J. Safra Bioinformatics Center at Tel Aviv University. We thank D. Hollander for consultation throughout the process of writing the manuscript. The research was funded by the Israel Science Foundation [ISF 671/18, ISF 142/13, and ISF 2417/20]; German-Israeli Foundation for Scientific Research and Development [GIF I-1460]; Israel Cancer Association [ICA 20170034]; Israel Cancer Research Fund [ICRF PG-18-105]; and United States ? Israel Binational Science Foundation [BSF 2017086]. L.T. was supported by a fellowship from the Planning & Budgeting Committee of the Council of Higher Education of Israel. O.H. and V.R.R. were supported by a fellowship from the Edmond J. Safra Bioinformatics Center at Tel Aviv University. We thank D. Hollander for consultation throughout the process of writing the manuscript. L.T. designed and performed the biological experiments. O.H. designed and performed the bioinformatics analyses related to the regulation of SFs in the nuclear periphery and center. I.K. constructed the Chrom3D models for HeLa, K562 and GM12878 cells. I.K. and O.H. performed the bioinformatics analyses related to the chromatin 3D models. V.R.R. constructed the 3D models of the LMNB1 KO and WT in MDA-MB-231 cells and O.H. performed the following RNA-seq analysis. N.C. and J.R. performed the FISH experiment with the endogenous genes. R.S. performed ChIP-seq of lamin A/C and generated the peripheral FRT-site using CRISPR-Cas9. A.A.T. and L.T. performed the FISH experiment with integrated minigenes. I.S. and O.H. performed the analyses of the peripheral and central subnetworks. V.R.-V. performed the evolutionary analyses. G.L.M. helped with constructing additional inserts and minigene cloning. Y.L. and L.T. performed the RT-qPCR. D.K. performed the intron shortening of the constructs. E.L.A and R.E. advised and guided in the design of the bioinformatics analyses. L.T. O.H. V.R.R. I.K. and G.A. wrote the manuscript. All authors mentioned above had the opportunity to edit, comment on, and approve the manuscript. The authors declare no competing interests. We worked to ensure diversity in experimental samples through the selection of the cell lines and genomic datasets. One or more of the authors of this paper self-identifies as an underrepresented ethnic minority in science. One or more of the authors of this paper received support from a program designed to increase minority representation in science. The author list of this paper includes contributors from the location where the research was conducted, and those who participated in the data collection, design, analysis, and/or interpretation of the work.

FundersFunder number
Edmond J. Safra Bioinformatics Center
RT-qPCR
Israel Cancer Research FundICRF PG-18-105
United States - Israel Binational Science FoundationBSF 2017086
German-Israeli Foundation for Scientific Research and DevelopmentGIF I-1460
United States-Israel Binational Science Foundation
Israel Cancer AssociationICA 20170034
Israel Science FoundationISF 2417/20, ISF 671/18, ISF 142/13
Tel Aviv UniversityK562, GM12878
Council for Higher Education

    Keywords

    • 3D genome
    • GC content
    • alternative splicing
    • exon definition
    • exon skipping
    • gene architecture
    • intron definition
    • intron retention
    • nuclear localization
    • splicing factors

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